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- PDB-3zos: Structure of the DDR1 kinase domain in complex with ponatinib -

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Basic information

Entry
Database: PDB / ID: 3zos
TitleStructure of the DDR1 kinase domain in complex with ponatinib
ComponentsEPITHELIAL DISCOIDIN DOMAIN-CONTAINING RECEPTOR 1
KeywordsTRANSFERASE / RTK / COLLAGEN / DISCOIDIN DOMAIN
Function / homology
Function and homology information


smooth muscle cell-matrix adhesion / regulation of extracellular matrix disassembly / regulation of cell-matrix adhesion / ear development / collagen-activated tyrosine kinase receptor signaling pathway / branching involved in mammary gland duct morphogenesis / wound healing, spreading of cells / neuron projection extension / smooth muscle cell migration / axon development ...smooth muscle cell-matrix adhesion / regulation of extracellular matrix disassembly / regulation of cell-matrix adhesion / ear development / collagen-activated tyrosine kinase receptor signaling pathway / branching involved in mammary gland duct morphogenesis / wound healing, spreading of cells / neuron projection extension / smooth muscle cell migration / axon development / Non-integrin membrane-ECM interactions / mammary gland alveolus development / peptidyl-tyrosine autophosphorylation / collagen binding / transmembrane receptor protein tyrosine kinase activity / lactation / embryo implantation / cell surface receptor protein tyrosine kinase signaling pathway / regulation of cell growth / placental growth factor receptor activity / insulin receptor activity / vascular endothelial growth factor receptor activity / hepatocyte growth factor receptor activity / macrophage colony-stimulating factor receptor activity / platelet-derived growth factor alpha-receptor activity / platelet-derived growth factor beta-receptor activity / stem cell factor receptor activity / boss receptor activity / protein tyrosine kinase collagen receptor activity / brain-derived neurotrophic factor receptor activity / transmembrane-ephrin receptor activity / GPI-linked ephrin receptor activity / epidermal growth factor receptor activity / fibroblast growth factor receptor activity / insulin-like growth factor receptor activity / receptor protein-tyrosine kinase / positive regulation of neuron projection development / protein autophosphorylation / cell population proliferation / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / cell adhesion / negative regulation of cell population proliferation / extracellular space / extracellular exosome / ATP binding / metal ion binding / plasma membrane
Similarity search - Function
: / Discoidin domain-containing receptor 1/2, DS-like domain / Coagulation factors 5/8 type C domain (FA58C) signature 2. / Coagulation factors 5/8 type C domain (FA58C) signature 1. / Coagulation factor 5/8 C-terminal domain, discoidin domain / Coagulation factors 5/8 type C domain (FA58C) profile. / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain / Tyrosine-protein kinase, receptor class II, conserved site / Receptor tyrosine kinase class II signature. ...: / Discoidin domain-containing receptor 1/2, DS-like domain / Coagulation factors 5/8 type C domain (FA58C) signature 2. / Coagulation factors 5/8 type C domain (FA58C) signature 1. / Coagulation factor 5/8 C-terminal domain, discoidin domain / Coagulation factors 5/8 type C domain (FA58C) profile. / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain / Tyrosine-protein kinase, receptor class II, conserved site / Receptor tyrosine kinase class II signature. / : / Galactose-binding-like domain superfamily / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-0LI / Epithelial discoidin domain-containing receptor 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsCanning, P. / Elkins, J.M. / Goubin, S. / Mahajan, P. / Bradley, A. / Coutandin, D. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Bullock, A.
CitationJournal: J.Mol.Biol. / Year: 2014
Title: Structural Mechanisms Determining Inhibition of the Collagen Receptor Ddr1 by Selective and Multi-Targeted Type II Kinase Inhibitors
Authors: Canning, P. / Elkins, J.M. / Goubin, S. / Mahajan, P. / Bradley, A. / Coutandin, D. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Bullock, A.
History
DepositionFeb 22, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 1, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 23, 2014Group: Database references
Revision 1.2May 7, 2014Group: Database references
Revision 1.3Jun 18, 2014Group: Database references
Revision 1.4Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.5Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_database_status / pdbx_entity_nonpoly / pdbx_initial_refinement_model / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: EPITHELIAL DISCOIDIN DOMAIN-CONTAINING RECEPTOR 1
B: EPITHELIAL DISCOIDIN DOMAIN-CONTAINING RECEPTOR 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,2928
Polymers71,5082
Non-polymers1,7846
Water6,053336
1
A: EPITHELIAL DISCOIDIN DOMAIN-CONTAINING RECEPTOR 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9435
Polymers35,7541
Non-polymers1,1894
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: EPITHELIAL DISCOIDIN DOMAIN-CONTAINING RECEPTOR 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3493
Polymers35,7541
Non-polymers5952
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.951, 61.733, 80.193
Angle α, β, γ (deg.)90.00, 104.40, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein EPITHELIAL DISCOIDIN DOMAIN-CONTAINING RECEPTOR 1 / EPITHELIAL DISCOIDIN DOMAIN RECEPTOR / CD167 ANTIGEN-LIKE FAMILY MEMBER A / CELL ADHESION KINASE / ...EPITHELIAL DISCOIDIN DOMAIN RECEPTOR / CD167 ANTIGEN-LIKE FAMILY MEMBER A / CELL ADHESION KINASE / DISCOIDIN RECEPTOR TYROSINE KINASE / HGK2 / MAMMARY CARCINOMA KINASE 10 / MCK-10 / PROTEIN-TYROSINE KINASE 3A / PROTEIN-TYROSINE KINASE RTK-6 / TRK E / TYROSINE KINASE DDR / TYROSINE-PROTEIN KINASE CAK / CD167A


Mass: 35754.094 Da / Num. of mol.: 2 / Fragment: KINASE DOMAIN, RESIDUES 601-913
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Description: MAMMALIAN GENE COLLECTION (MGC) / Plasmid: PFB-LIC-BSE / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm)
References: UniProt: Q08345, receptor protein-tyrosine kinase
#2: Chemical ChemComp-0LI / 3-(imidazo[1,2-b]pyridazin-3-ylethynyl)-4-methyl-N-{4-[(4-methylpiperazin-1-yl)methyl]-3-(trifluoromethyl)phenyl}benzam ide / Ponatinib


Mass: 532.559 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C29H27F3N6O / Comment: medication*YM
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 336 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.89 % / Description: NONE
Crystal growDetails: 0.1M BIS-TRIS PH 5.5, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jan 30, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.92→45.37 Å / Num. obs: 49502 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 6.1 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 9.1
Reflection shellResolution: 1.92→1.97 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.78 / Mean I/σ(I) obs: 2.7 / % possible all: 98.7

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4AT5

4at5


Resolution: 1.92→45.41 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.918 / SU B: 7.697 / SU ML: 0.117 / Cross valid method: THROUGHOUT / ESU R: 0.181 / ESU R Free: 0.153 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23416 2507 5.1 %RANDOM
Rwork0.20613 ---
obs0.20757 46866 98.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.707 Å2
Baniso -1Baniso -2Baniso -3
1-1.91 Å20 Å20.57 Å2
2---0.87 Å20 Å2
3----1.05 Å2
Refinement stepCycle: LAST / Resolution: 1.92→45.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4730 0 129 336 5195
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0195011
X-RAY DIFFRACTIONr_bond_other_d0.0040.024678
X-RAY DIFFRACTIONr_angle_refined_deg1.4881.9896822
X-RAY DIFFRACTIONr_angle_other_deg1.033310684
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.835610
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.47323.648233
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.19615786
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5151539
X-RAY DIFFRACTIONr_chiral_restr0.0870.2735
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0215704
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021205
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.92→1.97 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 185 -
Rwork0.368 3392 -
obs--97.2 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.4590.54420.93931.8772-0.91128.08270.07540.18250.1374-0.1195-0.10960.1038-0.3048-0.35070.03430.1240.0544-0.01420.2404-0.10070.1745-19.65118.1325-49.1023
26.69764.31524.2753.21442.36933.4841-0.2433-0.09580.1231-0.5036-0.10450.0023-0.1496-0.3060.34780.44370.2492-0.07240.2575-0.08330.1515-12.614910.1699-45.5393
32.6321-2.33280.12192.2429-0.1622.08130.10440.113-0.094-0.2912-0.16040.2062-0.0542-0.29640.0560.20360.0362-0.12710.1389-0.07820.1075-10.9373-2.1694-43.9248
41.059-0.5876-0.05891.22030.41721.6764-0.00440.0579-0.05430.0222-0.10540.2290.0019-0.19630.10980.0407-0.01950.01740.0358-0.02590.0541-4.3549-4.3199-34.5815
51.13930.1653-0.46833.40660.34722.8347-0.041-0.0776-0.06260.4215-0.0094-0.03970.09390.10770.05040.09380.01640.02010.01170.01220.01614.8702-11.6209-27.5317
64.95051.0271-1.37424.3947-2.8635.9143-0.01430.1821-0.0618-0.0714-0.23170.00560.511-0.51520.2460.1084-0.03010.03840.2145-0.12220.1503-28.7076.8375-9.4629
71.6759-1.6436-1.36775.6787-2.084616.5951-0.2216-0.11720.21370.33680.2327-0.2771-0.3749-0.7299-0.01110.14-0.03150.03140.363-0.09060.266-33.323210.89564.6543
82.1294-0.4951-1.08792.68591.24331.5074-0.03630.1805-0.28140.164-0.18720.17180.3093-0.45340.22360.145-0.11440.04090.196-0.03880.1291-20.91744.5-6.6381
97.56832.9211-2.220317.3402-0.71393.47120.2216-0.17370.5362-0.1704-0.18530.407-0.5651-0.284-0.03630.1130.0594-0.03940.1478-0.03840.1108-19.827731.3753-9.7775
100.83060.4284-0.1882.21570.17661.6825-0.02840.0237-0.0036-0.2729-0.0314-0.0562-0.13320.00520.05980.07360.0108-0.00950.0033-0.00090.0089-3.908122.9703-11.7131
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A602 - 638
2X-RAY DIFFRACTION2A639 - 677
3X-RAY DIFFRACTION3A678 - 734
4X-RAY DIFFRACTION4A735 - 813
5X-RAY DIFFRACTION5A814 - 913
6X-RAY DIFFRACTION6B-1 - 627
7X-RAY DIFFRACTION7B628 - 650
8X-RAY DIFFRACTION8B651 - 703
9X-RAY DIFFRACTION9B704 - 735
10X-RAY DIFFRACTION10B736 - 913

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